High resolution localization of single-copy nucleic acid sequences by fluorescence in situ hybridization has been described. See, e.g., Lawrence et al., Cell, 52: 51-61 (1988). Such methodology, however, is based on the use of a heterogenous population of relatively large probes, i.e., typically up to about 1,000 nucleotides. The probes, typically labeled by nick translation, carry undefined numbers of fluorochromes. The probes typically are designed to hybridize end-to-end, along a sequence of several thousand nucleotides within or near the target gene. In addition, such probes can hybridize to one another, forming large random aggregations due to "networking" at the target gene.
Although such methodology can detect the presence of a single copy of a nucleotide target sequence, the target sequence must be several thousand nucleotides long. Moreover, there is no stoichiometric relationship between the target sequence and fluorescence intensity.